FAIRsharing record for: ModelSEED Biochemistry Database

This FAIRsharing record describes: For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. The ModelSEED biochemistry database is the foundation of the biochemical data underlying ModelSEED and KBase. The The ModelSEED biochemistry database (i) includes compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) is extensible by the user community, with all data stored in GitHub; and (iii) designed as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes.